Transcription factors modulate RNA polymerase conformational equilibrium

Area of Science:

• Molecular Biology
• Structural Biology
• Genetics

Background:

• RNA polymerase (RNAP) pausing is a crucial mechanism for gene expression regulation.
• Transcription factors NusA and NusG are known to modulate RNAP pausing with opposing roles.
• These factors can bind to RNAP simultaneously, suggesting complex regulatory interactions.

Purpose of the Study:

• To elucidate the structural mechanisms by which NusA and NusG modulate RNAP pausing and transcription termination.
• To provide a structural basis for the opposing roles of NusA and NusG in regulating transcriptional pauses.
• To investigate the cooperative mechanism of NusA and NusG in Rho-mediated transcription termination.

Main Methods:

• Cryo-electron microscopy (cryo-EM) reconstructions of Escherichia coli RNAP.
• Structural analysis of RNAP bound to NusG, NusA, or both.
• Correlating RNAP conformational changes (swiveling) with transcriptional pausing.

Main Results:

• Detailed structures of RNAP bound to NusA, NusG, or both were obtained.
• RNAP swiveling, a conformational change, correlates with transcriptional pausing.
• NusA enhances RNAP swiveling and pausing, whereas NusG counteracts this effect.
• Structural findings align with biochemical data on different types of transcriptional pauses.
• Cooperative roles of NusA and NusG in Rho-mediated termination were suggested.

Conclusions:

• The study provides a structural rationale for how NusA and NusG modulate RNAP pausing and transcription termination.
• The findings explain the stochastic nature of pausing and termination through the actions of these factors.
• Understanding these mechanisms offers insights into gene expression regulation at the transcriptional level.